Target (protein/gene name): D-alanine ligase (K. pneumoniae) NCBI Gene # or RefSeq#: Protein ID (NP or XP #) or Wolbachia#: Organism (including strain): K. pneumoniae Etiologic Risk Group (see link below): Disease Information (sort of like the Intro to your Mini Research Write up):
K. pneumoniae affects mostly middle ages and older men with debilitating diseases (those with weakened immune systems). The bacteria enters the body through the lungs. The bacteria causes pneumonia and bronchitis. The death rate is around 50%, and up to 100% for people with alcoholism and bacteremia.
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)
Essentiality of this protein:
Typical antibiotics such as penicillin already attack the components of bacterial cell walls. D-alanine ligase catalyzes the dipeptide d-alanyl-d-alanine, which is an essential building block for cell wall synthesis. Is it a monomer or multimer as biological unit? 3I12=dimer, 3RFC=dimer Complex of proteins?: Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): Malachite Green Phosphate Assay $77 -- link to Sigma (or other company) page for assay (see Sigma links below) https://www.caymanchem.com/product/10009325 -- -or link (or citation) to paper that contains assay information -- links to assay reagents (substrates) pages. --- List cost and quantity of substrate reagents, supplier, and catalog # https://www.caymanchem.com/pdfs/10009325.pdf
Structure (PDB or Homology model) -- PDB # or closest PDB entry if using homology model:
PDB 3I12 (96% query cover, 86% ident), PDB 3RFC (98% query cover, 63% ident) ---- Show pairwise alignment of your BLASTP search in NCBI against the PDB:
Current Inhibitors: Some inhibitors have been found here, mostly those that replace ATP. BRENDA also displays numerous inhibitors, but not for this specific species. Expression Information (has it been expressed in bacterial cells): Purification Method: Image of protein (PyMol with features delineated and shown separately): 3RFC
3I12
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): *length of your protein in Amino Acids: Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: Molar Extinction coefficient of your protein at 280 nm wavelength: TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
*GC% Content for gene: *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
Primer design results for 'tail' primers (this is just 2 sequences): Ordered and designed by Marissa Hansen
NCBI Gene # or RefSeq#:
Protein ID (NP or XP #) or Wolbachia#:
Organism (including strain): K. pneumoniae
Etiologic Risk Group (see link below):
Disease Information (sort of like the Intro to your Mini Research Write up):
K. pneumoniae affects mostly middle ages and older men with debilitating diseases (those with weakened immune systems). The bacteria enters the body through the lungs. The bacteria causes pneumonia and bronchitis. The death rate is around 50%, and up to 100% for people with alcoholism and bacteremia.
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)
Essentiality of this protein:
Typical antibiotics such as penicillin already attack the components of bacterial cell walls. D-alanine ligase catalyzes the dipeptide d-alanyl-d-alanine, which is an essential building block for cell wall synthesis.
Is it a monomer or multimer as biological unit? 3I12=dimer, 3RFC=dimer
Complex of proteins?:
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):
EC#: 6.3.2.4
Link to BRENDA EC# page:
http://www.brenda-enzymes.org/enzyme.php?ecno=6.3.2.4
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): Malachite Green Phosphate Assay $77
-- link to Sigma (or other company) page for assay (see Sigma links below)
https://www.caymanchem.com/product/10009325
-- -or link (or citation) to paper that contains assay information
-- links to assay reagents (substrates) pages.
--- List cost and quantity of substrate reagents, supplier, and catalog #
https://www.caymanchem.com/pdfs/10009325.pdf
Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model:
PDB 3I12 (96% query cover, 86% ident), PDB 3RFC (98% query cover, 63% ident)
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB:
Current Inhibitors: Some inhibitors have been found here, mostly those that replace ATP. BRENDA also displays numerous inhibitors, but not for this specific species.
Expression Information (has it been expressed in bacterial cells):
Purification Method:
Image of protein (PyMol with features delineated and shown separately):
3RFC
3I12
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
*length of your protein in Amino Acids:
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website:
Molar Extinction coefficient of your protein at 280 nm wavelength:
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
*GC% Content for gene:
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
Primer design results for 'tail' primers (this is just 2 sequences): Ordered and designed by Marissa Hansen